Subject: Epigenetics ==================== * Histone methylation makes its mark on longevity. 2011 Shuo Han and Anne Brunet. Han11_histone_modification_longevity.pdf --- * On the connection between RNAi and heterochromatin at centromeres. 2010 Lejeune E, Bayne EH and Allshire RC. Lejeune11_RNAi_heterochromatin.pdf --- * Theory for the stability and regulation of epigenetic landscapes. 2010 Mille A Micheelsen, Namiko Mitarai, Kim Sneppen and Ian B Dodd. Micheelsen10_epigenetic_landscapes.pdf --- * Defining an epigenetic code. 2007 Bryan M. Turner. Turner07_epigenetic_code.pdf --- * Genomic characterization reveals a simple histone H4 acetylation code. 2005 Michael F. Dion, Steven J. Altschuler, Lani F. Wu, and Oliver J. Rando. Dion05_histone_combinatorics.pdf and Histone modifications: Combinatorial complexity or cumulative simplicity? 2005 Steven Henikoff. Henikoff05_histone_combinatorics.pdf --- * Histone exchange and histone modifications during transcription and aging. 2011 Chandrima Das and Jessica K. Tyler. Das11_histone_exchange_aging.pdf --- * Barriers and Silencers: A Theoretical Toolkit for Control and Containment of Nucleosome-Based Epigenetic States. 2011 Ian B. Dodd and Kim Sneppen. Dodd11_epigenetic_model.pdf (for one or two students) Subject: Transcription Factor Binding ===================================== * Evolutionary Origins of Transcription Factor Binding Site Clusters. 2011 He X, Duque TS and Sinha S. He11_TFBS_cluster.pdf --- * Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. 2010 Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA and Ovcharenko I. Gotea10_homotypic_clusters_TFBS.pdf --- * Models of transcription factor binding: Sensitivity of activation functions to model assumptions. 2009 Dominique Chu, Nicolae Radu Zabet and Boris Mitavskiy. Chu09_TF_binding_models.pdf --- * Maximally Efficient Modeling of DNA Sequence Motifs at All Levels of Complexity. 2011 Gary D. Stormo. Stormo11_PWM_simplex.pdf ---